Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Spatial" keyword
standR 1.6.0
Spatial transcriptome analyses of Nanostring's DSP data in R3 versions - Latest release: 6 months ago - 3.38 thousand downloads total - 15 stars on GitHub - 1 maintainer
DESpace 1.2.1
DESpace: a framework to discover spatially variable genes4 versions - Latest release: 3 months ago - 1.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
pengls 1.8.0
Fit Penalised Generalised Least Squares models3 versions - Latest release: 6 months ago - 2.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
stJoincount 1.4.0
stJoincount - Join count statistic for quantifying spatial correlation between clusters3 versions - Latest release: 6 months ago - 1.81 thousand downloads total - 5 stars on GitHub - 1 maintainer
Voyager 1.4.0
From geospatial to spatial omics3 versions - Latest release: 6 months ago - 2.86 thousand downloads total - 60 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.2.1
Spatial Overlay for Omic Data from Nanostring GeoMx Data3 versions - Latest release: 6 months ago - 1.68 thousand downloads total - 1 maintainer
CTSV 1.4.0
Identification of cell-type-specific spatially variable genes accounting for excess zeros3 versions - Latest release: 6 months ago - 1.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
miRspongeR 2.6.0
Identification and analysis of miRNA sponge regulation3 versions - Latest release: 6 months ago - 1 dependent package - 6.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
FuseSOM 1.4.0
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets3 versions - Latest release: 6 months ago - 1.79 thousand downloads total - 1 stars on GitHub - 1 maintainer
tomoseqr 1.6.0
R Package for Analyzing Tomo-seq Data3 versions - Latest release: 6 months ago - 1.82 thousand downloads total - 1 maintainer
tidySpatialExperiment 1.0.0
Brings SpatialExperiment to the tidyverse2 versions - Latest release: 7 days ago - 347 downloads total - 4 stars on GitHub - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation4 versions - Latest release: 14 days ago - 1.88 thousand downloads total - 0 stars on GitHub - 1 maintainer
GeomxTools 3.6.2
NanoString GeoMx Tools4 versions - Latest release: 3 months ago - 3 dependent packages - 15.9 thousand downloads total - 1 maintainer
STdeconvolve 1.6.0
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data3 versions - Latest release: 6 months ago - 3.66 thousand downloads total - 1 maintainer
SpaceMarkers 1.0.0
Spatial Interaction Markers1 version - Latest release: 23 days ago - 255 downloads total - 0 stars on GitHub - 1 maintainer
signifinder 1.4.0
Collection and implementation of public transcriptional cancer signatures3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
nnSVG 1.6.4
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data5 versions - Latest release: about 1 month ago - 2 dependent packages - 3.17 thousand downloads total - 10 stars on GitHub - 1 maintainer
SpatialFeatureExperiment 1.6.1
Integrating SpatialExperiment with Simple Features in sf4 versions - Latest release: 12 days ago - 1 dependent package - 4.09 thousand downloads total - 21 stars on GitHub - 1 maintainer
imcRtools 1.10.0
Methods for imaging mass cytometry data analysis3 versions - Latest release: 8 days ago - 1 dependent package - 7.22 thousand downloads total - 18 stars on GitHub - 1 maintainer
spatialHeatmap 2.10.0
spatialHeatmap8 versions - Latest release: 8 days ago - 5.78 thousand downloads total - 4 stars on GitHub - 1 maintainer
Banksy 1.0.0
Spatial transcriptomic clustering1 version - Latest release: 23 days ago - 390 downloads total - 45 stars on GitHub - 1 maintainer
mistyR 1.12.0
Multiview Intercellular SpaTial modeling framework4 versions - Latest release: 9 days ago - 4.1 thousand downloads total - 39 stars on GitHub - 1 maintainer
scider 1.2.0
Spatial cell-type inter-correlation by density in R2 versions - Latest release: 21 days ago - 888 downloads total - 0 stars on GitHub - 1 maintainer
retrofit 1.4.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics3 versions - Latest release: 22 days ago - 1.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
scDesign3 1.2.0
A unified framework of realistic in silico data generation and statistical model inference for si...3 versions - Latest release: 9 days ago - 883 downloads total - 59 stars on GitHub - 1 maintainer
hoodscanR 1.2.0
Spatial cellular neighbourhood scanning in R2 versions - Latest release: 10 days ago - 841 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 18 days ago - 36 dependent packages - 57.5 thousand downloads total - 45 stars on GitHub - 1 maintainer
SpatialExperiment 1.14.0
S4 Class for Spatially Resolved -omics Data3 versions - Latest release: 18 days ago - 36 dependent packages - 57.5 thousand downloads total - 45 stars on GitHub - 1 maintainer
ggspavis 1.9.10
Visualization functions for spatial transcriptomics data4 versions - Latest release: 22 days ago - 1 dependent package - 4.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
escheR 1.3.2
Unified multi-dimensional visualizations with Gestalt principles3 versions - Latest release: 15 days ago - 2 dependent packages - 1.93 thousand downloads total - 3 stars on GitHub - 1 maintainer
SpatialDecon 1.14.0
Deconvolution of mixed cells from spatial and/or bulk gene expression data4 versions - Latest release: 12 days ago - 1 dependent package - 8.19 thousand downloads total - 27 stars on GitHub - 1 maintainer
ggsc 1.2.0
Visualizing Single Cell and Spatial Transcriptomics3 versions - Latest release: 12 days ago - 930 downloads total - 30 stars on GitHub - 1 maintainer
SpotClean 1.6.0
SpotClean adjusts for spot swapping in spatial transcriptomics data4 versions - Latest release: 14 days ago - 2.83 thousand downloads total - 13 stars on GitHub - 1 maintainer
scatterHatch 1.10.0
Creates hatched patterns for scatterplots3 versions - Latest release: 14 days ago - 1.96 thousand downloads total - 5 stars on GitHub - 1 maintainer
scFeatures 1.4.0
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome predic...4 versions - Latest release: 14 days ago - 1.45 thousand downloads total - 10 stars on GitHub - 1 maintainer
Statial 1.6.0
A package to identify changes in cell state relative to spatial associations6 versions - Latest release: 16 days ago - 1.84 thousand downloads total - 1 stars on GitHub - 1 maintainer
smoothclust 0.99.8
smoothclust1 version - Latest release: 23 days ago - 162 downloads total - 0 stars on GitHub - 1 maintainer
SPOTlight 1.8.0
`SPOTlight`: Spatial Transcriptomics Deconvolution5 versions - Latest release: 19 days ago - 6.1 thousand downloads total - 139 stars on GitHub - 1 maintainer
MoleculeExperiment 1.4.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data5 versions - Latest release: 19 days ago - 1.44 thousand downloads total - 10 stars on GitHub - 1 maintainer
SPIAT 1.6.0
Spatial Image Analysis of Tissues5 versions - Latest release: 22 days ago - 2.95 thousand downloads total - 16 stars on GitHub - 1 maintainer
spaSim 1.6.0
Spatial point data simulator for tissue images3 versions - Latest release: 22 days ago - 1.61 thousand downloads total - 1 stars on GitHub - 1 maintainer
betaHMM 1.0.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...1 version - Latest release: 23 days ago - 175 downloads total - 1 maintainer
spoon 0.99.10
Address the Mean-variance Relationship in Spatial Transcriptomics Data1 version - Latest release: 23 days ago - 154 downloads total - 0 stars on GitHub - 1 maintainer
VisiumIO 1.0.0
Import Visium data from the 10X Space Ranger pipeline1 version - Latest release: 23 days ago - 169 downloads total - 0 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes1 version - Latest release: 23 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
SpotSweeper 0.99.5
Spatially-aware quality control for spatial transcriptomics1 version - Latest release: 23 days ago - 0 stars on GitHub - 1 maintainer
RegionalST 1.0.1
Investigating regions of interest and performing cross-regional analysis with spatial transcripto...2 versions - Latest release: 5 months ago - 750 downloads total - 1 maintainer
tomoda 1.12.0
Tomo-seq data analysis2 versions - Latest release: 6 months ago - 2.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
lisaClust 1.10.1
lisaClust: Clustering of Local Indicators of Spatial Association2 versions - Latest release: 6 months ago - 1 dependent package - 4.88 thousand downloads total - 3 stars on GitHub - 1 maintainer
cytoviewer 1.2.0
An interactive multi-channel image viewer for R2 versions - Latest release: 7 months ago - 1.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
spicyR 1.14.3
Spatial analysis of in situ cytometry data3 versions - Latest release: 4 months ago - 2 dependent packages - 7.24 thousand downloads total - 8 stars on GitHub - 1 maintainer
Related Keywords
Software
50
SingleCell
31
Transcriptomics
30
GeneExpression
27
Visualization
13
RNASeq
11
Clustering
9
DataImport
9
Sequencing
9
ImmunoOncology
7
CellBasedAssays
7
BiomedicalInformatics
6
StatisticalMethod
5
DataRepresentation
5
DimensionReduction
5
r
5
Microarray
4
Infrastructure
4
Preprocessing
4
CellBiology
4
Regression
4
QualityControl
4
GeneTarget
3
bioconductor
3
spatial
3
spatial-transcriptomics
3
single-cell
3
Normalization
3
FeatureExtraction
2
Bayesian
2
visualization
2
Classification
2
Survival
2
spatial-omics
2
DifferentialExpression
2
Transcription
2
Proteomics
2
ProprietaryPlatforms
2
spatial-statistics
2
rstats
2
OneChannel
1
molecular-biology
1
TwoChannel
1
modular
1
imaging
1
machine-learning
1
intercellular
1
biology
1
SystemsBiology
1
shiny
1
DecisionTree
1
multiview
1
MultiChannel
1
Reactome
1
KEGG
1
MultipleComparison
1
multidimensional
1
MethylationArray
1
rna-seq
1
Coverage
1
DNAMethylation
1
DifferentialMethylation
1
HiddenMarkovModel
1
ExperimentHubSoftware
1
TimeCourse
1
BiocViews
1
eda
1
esda
1
exploratory-data-analysis
1
omics
1
r-package
1
transcriptomics
1
Genetics
1
NetworkEnrichment
1
cerna
1
mirna
1
sponge
1
ExperimentalDesign
1
mRNAMicroarray
1
GeneSignaling
1
ReportWriting
1
imc
1
ATACSeq
1
DNASeq
1
GraphAndNetwork
1
Network
1
TissueMicroarray
1
clustering-algorithm
1
single-cell-omics
1